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Yorodumi- PDB-5dv2: Crystal structure of human CNOT6L in complex with cytidine-5'-mon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dv2 | ||||||
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Title | Crystal structure of human CNOT6L in complex with cytidine-5'-monophosphate | ||||||
Components | CCR4-NOT transcription complex subunit 6-like | ||||||
Keywords | HYDROLASE / nuclease domain / deadenylase / INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA processing ...positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA processing / regulation of translation / positive regulation of cell population proliferation / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Zhang, Q. / Bartlam, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Febs Lett. / Year: 2016 Title: Structural basis for inhibition of the deadenylase activity of human CNOT6L Authors: Zhang, Q. / Yan, D. / Guo, E. / Ding, B. / Yang, W. / Liu, R. / Yamamoto, T. / Bartlam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dv2.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dv2.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 5dv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/5dv2 ftp://data.pdbj.org/pub/pdb/validation_reports/dv/5dv2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45140.500 Da / Num. of mol.: 1 / Fragment: UNP residues 158-555 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT6L, CCR4B / Production host: Escherichia coli (E. coli) / References: UniProt: Q96LI5, poly(A)-specific ribonuclease |
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#2: Chemical | ChemComp-C5P / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 1.1M ammonium tartrate, 0.2M NDSB-201 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 35967 / % possible obs: 99.9 % / Redundancy: 6.3 % / Net I/σ(I): 29.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→42.843 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→42.843 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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